Marine biomonitoring from environmental DNA
The analysis of biological molecules (e.g. DNA, RNA, proteins) from marine samples is a powerful new technique for marine biomonitoring, called Environmental DNA (eDNA) analysis. Environmental DNA (eDNA) is the DNA of whole or partial organisms, organismal traces (e.g. skin, mucus, and feces), or microbes in an environmental sample. It includes DNA from marine microbiomes, plankton, and traces of marine animals. By examining DNA fragments secreted by organisms into the environment, eDNA analysis allows for the detection and monitoring of species in their natural habitats using molecular biology techniques. These techniques are based on sequencing and analyzing DNA and comparing the information obtained with existing reference libraries to identify species. It includes metabarcoding (sequencing a selected gene fragment from a group of organisms such as all fish or bacteria) and quantitative polymerase chain reaction (qPCR). Polymerase chain reaction (PCR) is a widely used amplification method. It allows millions to billions of copies of a specific DNA sample to be rapidly made to detect and quantify gene expression by comparison with reference genomes from a DNA library. For both animals and microorganisms, metabarcoding can reveal the presence (or absence) and in some cases the relative abundance of species in a water sample, and with qPCR it is in some cases able to quantify the number of individuals present or recently present in a given volume of water. Analysis of eDNA allows detection of essentially any organism from trace DNA evidence, assessment of the relative or absolute abundance of certain groups, and accurate taxonomic assignment if reference genomes are available.[1]
A limitation of applying polymerase chain reaction (PCR) for DNA amplification is the so-called PCR bias. This is the overestimation of the importance of certain taxa and failure to detect other taxa because they do not amplify to the same extent. [2]
Metagenomics is an eDNA method that avoids the PCR bias. Metagenomics analyzes genetic material extracted directly from an environmental sample, by random sequencing ('shotgun sequencing') of the entire genomic DNA (the metagenome). It is an efficient method to investigate the diversity of microbial communities and their functional capacities. Metagenomics aids in the study of ecosystem dynamics and the assessment of environmental health. It can be used for monitoring environmental conditions to predict catastrophic and damaging environmental changes. However, it is not yet possible to reliably taxonomize all species present in the metagenome. This limitation of both metabarcoding and metagenomics is due to the current lack of comprehensive reference sequences, as only small parts of the genome have been sequenced for most species so far.[2]
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References
- ↑ Thompson, L.R. and Thielen, P. 2023. Decoding dissolved information: environmental DNA sequencing at global scale to monitor a changing ocean. Current Opinion in Biotechnology 81, 102936
- ↑ 2.0 2.1 Serite, C.P., Emami-Khoyi, A., Ntshudisane, O.K., James, N.C., Jansen van Vuuren, B., Bodill, T., Cowley, P.D., Whitfield, A.K. and Teske, P.R. 2023. eDNA metabarcoding vs metagenomics: an assessment of dietary competition in two estuarine pipefishes. Front. Mar. Sci. 10, 1116741
